RNAseq_UMG_SDumont_v1 Version 1
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Run on GalaxyRNAseq workflow UMG: Here we introduce a scientific workflow implementing several open-source software executed by Galaxy parallel scripting language in an high-performance computing environment. We have applied the workflow to a single-cardiomyocyte RNA-seq data retrieved from Gene Expression Omnibus database. The workflow allows for the analysis (alignment, QC, sort and count reads, statistics generation) of raw RNA-seq data and seamless integration of differential expression results into a configurable script code.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| GTF File | GTF File | n/a |
|
| KO Fastq Files | KO Fastq Files | n/a |
|
| WT Fastq Files | WT Fastq Files | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 3 | Align WT | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 |
| 4 | Align KO | toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0 |
| 5 | Counts WT | toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1 |
| 6 | Counts KO | toolshed.g2.bx.psu.edu/repos/lparsons/htseq_count/htseq_count/0.9.1 |
| 7 | DE Analysis WTvsKO | toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6 |
| 8 | CreateFilterOnCountsNA | Filter1 |
| 9 | CreateFilterOnCountsC7 | Filter1 |
| 10 | CreateSortOnCounts | sort1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| _anonymous_output_4 | _anonymous_output_4 | n/a |
|
| _anonymous_output_5 | _anonymous_output_5 | n/a |
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| _anonymous_output_6 | _anonymous_output_6 | n/a |
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| _anonymous_output_7 | _anonymous_output_7 | n/a |
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| _anonymous_output_8 | _anonymous_output_8 | n/a |
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| _anonymous_output_9 | _anonymous_output_9 | n/a |
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| _anonymous_output_10 | _anonymous_output_10 | n/a |
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| _anonymous_output_11 | _anonymous_output_11 | n/a |
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| _anonymous_output_12 | _anonymous_output_12 | n/a |
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| _anonymous_output_13 | _anonymous_output_13 | n/a |
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| _anonymous_output_14 | _anonymous_output_14 | n/a |
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| _anonymous_output_15 | _anonymous_output_15 | n/a |
|
| _anonymous_output_16 | _anonymous_output_16 | n/a |
|
| _anonymous_output_17 | _anonymous_output_17 | n/a |
|
Version History
Version 1 (earliest) Created 6th Dec 2022 at 19:22 by Kary Ocaña
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Version-1fc807ec
Creators and Submitter
Views: 3841 Downloads: 253 Runs: 0
Created: 6th Dec 2022 at 19:22
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https://orcid.org/0000-0002-2151-7418I am a bioinformatician and phylogenetics. I really love working on problems at the intersection of high-performance computing and scientific workflows applied to omics
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Here we introduce a scientific workflow implementing several open-source software executed by Parsl parallel scripting language in an high-performance computing environment. We have applied the workflow to a single-cardiomyocyte RNA-seq data retrieved from Gene Expression Omnibus database. The workflow allows for the analysis (alignment, QC, sort and count reads, statistics generation) of raw RNA-seq data and seamless integration of differential expression results into a configurable script code. ...
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